Level 2 Help for MARSREMOS

INP

There are two options for describing input images.

Either:
List the image file names

Or:
provide an ascii file with the file names listed, one per record.


OUT

Output image containing the mosaic.

By default, the output will have the same number of bands
as the input with the most bands, and all bands will be processed.  Inputs
with fewer than that many bands repeat their last band, so bw and color images
can be mixed.  If BAND is specified, the output will have a single band.


BAND

The BSQ input file band number. Defaults to all bands in image, but will use
a value of 1 if an invalid band is specified. Providing a value will cause
only that band to be processed.


INPUT_RANGE

The range of inputs to actually mosaic.  Normally all inputs are mosaicked.
However, if this parameter is specified, all inputs will be used to calculate
the output projection, but only the inputs in the specified range will be
mosaicked.  This allows the generation of a large mosaic to be spread out
over several nodes on a network, with a program like FASTMOS used to combine
all the outputs together.  Note that any underlays (annotation that goes
under the image) should be put on the *last* mosaic only for FASTMOS;
overlays (that show on top of everything) should be on all images (or at
least the first).

The input numbers are 1-based.  If only one number is specified, it is the
starting number; the end defaults to the # of inputs.


BRTCORR

Specifies an input file containing brightness corrections.  This is an
XML file that comes from a program like marsbrt which contains correction
factors for each image.  These factors may be additive or multiplicative
constants to be applied to the image, or other corrections that may be
implemented in the future.

The BRTCORR mechanism is intended to replace BIAS.  Using them together
should be avoided because the labels will not reflect both (the BIAS
overrides).  If you do, however, the BRTCORR corrections are applied to
the data first, before BIAS.


RAD

Keyword parameter that turns on or off radiometric correction of the input
images.  RAD (the default) enables the correction (for missions/instruments
which support it), while NORAD disables it.


DNSCALE

DN scaling factor.  This factor is used to convert between physical
radiometric units (watts/(meter**2, steradian, micron)) and DN's for the
output mosaic.  The formula is:

true_radiance = offset + (factor * DN)

where "offset" is 0.0 in the current implementation, and "factor" is
1.0 / DNSCALE (making the formula equivalently:  offset + (DN / DNSCALE)).
The offset and factor (1.0/DNSCALE) are written to the output mosaic label.


CONFIG_PATH

A colon-separated list of directories in which to look for configuration
and calibration files.  Environment variables are allowed in the list
(and may themselves contain colon-separated lists).  The directories are
searched in order for each config/cal file when it is loaded.  This allows
multiple projectes to be supported simultaneously, and allows the user to
override any given config/cal file.  Note that the directory structure below
the directories specified in this path must match what the project expects.
For example, Mars 98 expects flat fields to be in a subdirectory named
"flat_fields" while Mars Pathfinder expects them to be directly in the
directory specified by the path (i.e. no intermediate subdirectories).


POINT_METHOD

Specifies a mission-specific pointing method to use.  Normally this
parameter is not used, in which case the "default" pointing methods
are used.  Some missions may have special, or alternate, pointing
methods available, which are indicated by this string (for example,
backlash models, using arm joint angles instead of x/y/z/az/el, etc).
A substring search is used, so multiple methods (where that makes sense)
can be specified by separating the keywords with commas.

Note that nav files created using one pointing method will most likely
not be compatible with a mosaic created using a different pointing method.

The methods available vary per mission, but some methods available at
the time of this writing are:

BACKLASH : Mars 98 SSI only.  Selects a backlash pointing model,
which adjusts the telemetered azimuth and elevation values based on
knowledge of the camera's mechanical backlash and the direction the
motor was travelling when the image was taken.

Values useful to marsremos:

BORDER_LEFT:  Specifies, in pixels, a border to cut off on the left side of
  each input image.  This can be used to eliminate edge effects in input images.
BORDER_RIGHT:  Same but for the right side.
BORDER_TOP:  Same but for the top edge.
BORDER_BOTTOM:  Same but for the bottom edge.

New ones (as of 2012/10/26) not mentioned elsewhere:

RMC_MAX_INDEX: Specifies the max # of indices to use when comparing RMC's.
  Effectively makes the RMC only this long.  Useful to ignore pose changes
  due to IMU jitter, or when using the RSF file.  Default is 10.
RMC_EPSILON: Epsilon value for comparison of coordinate system values.  Even
  if the RMC's match, a new CS is created if the values differ by more than
  this epsilon.  Setting it high means more CS's will considered equal.
  Default: 1e-3
MARGIN_LEFT:  Like BORDER_LEFT, but the margin is scaled based on the
  downsample factor of the image.  So if the margin is needed to hide CCD
  defects, the same area of the CCD will be cut off regardless of downsampling.
MARGIN_RIGHT, MARGIN_TOP, MARGIN_BOTTOM:  Same as above.


NOSITE

Disables all label-derived parameters to the Site mechanism which underlies
coordinate systems.  This forces all sites to be identical, with all rotations
and offsets set the same.  In the case of MPF or Mars 98, this disables
the lander quaternion and offset (sets them to identity and 0, respectively).
This option should not be used with images taken from different vantage
points (e.g. the spacecraft moved, or mixing a lander and a rover) or
invalid results will be obtained.  The use of this option invalidates the
Fixed coordinate frame; any values reported in the Fixed frame will not
correctly reflect the orientation of the lander/rover.

Obviously, this option should be rarely used; it is intended for when the
image labels defining the site are invalid or inconsistent.


INTERP

Keyword parameter that turns on or off interpolation of the output
images pixel values.  INTERP (the default) enables the interpolation, 
while NOINTERP disables it.

MEMORY mode (the default) is somewhat faster (perhaps 10%, although
that's highly variable), and is required if doing parallel processing.
However, the memory requirements could become prohibitive for large
mosaics.

INCREMENTAL mode is slower, but has the advantage of being able to view
the mosaic as it is being generated.  An image viewer such as xvd can be
used to monitor the progress of the mosaic.  By reloading periodically,
one can do quality control while a long mosaic is in progress.  Also,
the memory requirements are drastically lower in this mode.


DATA_SET_NAME

The DATA_SET_NAME typically identifies the instrument that acquired the
data, the target of that instrument, and the processing level of the data.
This value is copied to the output label, property IDENTIFICATION, 
keyword DATA_SET_NAME.


DATA_SET_ID

The DATA_SET_ID value for a given data set or product is constructed
according to flight project naming conventions.  In most cases the 
DATA_SET_ID is an abbreviation of the DATA_SET_NAME.
This value is copied to the output label, property IDENTIFICATION, 
keyword DATA_SET_ID.


RELEASE_ID

When a data set is released incrementally, such as every three months during
a mission, the RELEASE_ID is updated each time part of the data set is released.
For each mission(or host id if multiple spacecrafts), the first release of a data
set should have a value of "0001".
This value is copied to the output label, property IDENTIFICATION, 
keyword RELEASE_ID.


PRODUCT_ID

Specifies a permanent, unique identifier assigned to a data product by 
its producer. Most commonly, it is the filename minus the extension.
This value is copied to the output label, property IDENTIFICATION, 
keyword PRODUCT_ID.


PRODUCER_ID

Specifies the unique identifier of an entity associated with the
production of a data set. This value is copied to the output label,
property IDENTIFICATION, keyword PRODUCER_ID.


PRODUCER_INST

Specifies the identity of a university, research center, NASA center or other
institution associated with the production of a data set.
This value is copied to the output label, property IDENTIFICATION, keyword 
PRODUCER_INSTITUTION_NAME.


TARGET_NAME

Specifies a target.  The target may be a planet, satelite, ring, region, feature,
asteroid or comet.  This value is copied to the output label, property
IDENTIFICATION, keyword TARGET_NAME.


TARGET_TYPE

Specifies the type of a named target. This value is copied to the output 
label, property IDENTIFICATION, keyword TARGET_NAME.


RSF

Rover State File.  This is a list of filenames to load containing
Rover State information.  These files contain position and orientation
information for a rover (or other mobile spacecraft) at various sites.
They are in XML format.  See the "Rover Motion Counter (RMC) Master File SIS"
for details on these files.

Rover State Files have a priority order.  The files listed first have
the highest priority.

Environment variables may be used in the list.

For MER, if a directory is specified, then that directory is searched for
RMC Master files and any found are loaded.  The directory structure and
filename convention is covered in the RMC SIS.  The directory specified
is the one containing "master", so if <dir> is the name specified in the
RSF parameter, the following files will be searched for:

<dir>/master/_Master.svf
<dir>/master/_Site__Master.rvf

The name of each file loaded is printed to the stdout log for reference.


DEBUG_RSF

If enabled, this causes the internal database of RMC locations to be
printed out to the stdout log.  This is after the RSF files have been
loaded and the coordinate systems read from the input label(s).


COORD

The coordinate system to use for all input parameters and output values,
and the mosaic itself.  The interpretation of the values is dependent on
the mission.  Some representative missions are listed here:

Fixed - The Fixed frame (default).  This is the ultimate reference frame
    (see also FIXED_SITE for rover missions).
Instrument - The "natural" frame for the instrument (of the first input
    image).  MPF: Lander or Rover; M98: MVACS; MER: Rover.
Site - A major Site frame.  For rover missions, COORD_INDEX specifies which
    Site frame to use.  Non-rover missions treat this as Fixed.
Rover - An instance of the Rover frame.  For rover missions, COORD_INDEX
    specifies which instance of the rover frame to use.  Non-rover mission
    use the spacecraft frame (e.g. Lander for M98).
Local_Level - An instance of a Local Level frame.  This is typically
    coincident with the Rover frame (in XYZ) but oriented toward North
    like the Site and Fixed frames.  For MER, this is an instance of a
    Drive index move.


COORD_INDEX

The index specifies which instance of a coordinate system to use.  It is
currently applicable only to rover-based missions, but could have other
uses.  The index is equivalent to the Rover Motion Counter (RMC) for MER
and FIDO.

For MER/FIDO, there are many Site frames.  Each is numbered with a single
index.  For Site Frames, coord_index specifies which to use.  Likewise,
there are many Local_Level and Rover frames, corresponding to values of
the RMC.  The multiple instances of this frame are selected by COORD_INDEX.

Generally COORD_INDEX defaults sensibly so you don't usually need to
specify it.  It will default to the instance used by the first input.


FIXED_SITE

Specifies which major Site is the "Fixed" Site for this run.

Historically, MPF and M98 had a single "Surface Fixed" frame which never
moved, and which all other coordinate system frames were referenced to.
With the advent of long-range rovers (such as MER and FIDO), that became
insufficient.  The rover traverses far enough that errors in knowledge of
coordinate system offset and orientation become unacceptable.

For this reason, a system of major Sites was introduced.  Periodically
during the mission, a Site frame is declared.  This then becomes the
reference frame for all activities until the next Site is declared.
References are kept local, and errors don't propogate across Sites.

However, if images from more than one Site are combined together, the
Site's must be placed relative to each other.  Therefore a single reference
frame is still needed to combine different sites.

The FIXED_SITE parameter controls which of the major Site frames is
the reference ("fixed") site for this program run.  This fixed frame
can vary in different program runs, but is constant throughout one
execution.

If not specified, FIXED_SITE defaults to the minimum Site number (i.e.
lowest numbered, or earliest chronologically) used in all input images.
Normally this default is sufficient; rarely must FIXED_SITE be specified.

One or more Rover State Files must usually be specified in order to combine
image from more than one Site.  These describe the relationship between
sites.  See the RSF parameter.


SOLUTION_ID

Specifies which solution ID to use for pointng corrections.

There are potentially many different definitions for the same coordinate
system. These are identified via a unique Solution ID.  If this parameter
is given, only the specified solution's definition is searched for.


MAX_OPEN

Specifies the number of images for each pass.  Normally this is 20.  Generally 
this will not need to be adjusted, but if the last pass has only one or two 
images, you may get better throughput by increasing this parameter slightly.
Each pass has an overhead, so if memory is sufficient, a large value can also 
increase throughput.


IDX

Specifies the input filename for the index file.

The index file contains, for each pixel, a halfword integer (16 bit signed)
identifying which image the pixel came from.  0 indicates no value (black
in the mosaic).  Numbers from 1-n match the order of files in the input list
file (or INP parameter, if a list file isn't given).  For most mosaics, the
file could be converted to byte using CFORM (half is used to support more
than 255 input files).


ICM

Specifies the input filename for the ICM file.

The ICM file is an Image Coregistration Map.  It is a two-band float file
containing the line, sample coordinate of the input pixel used for the point.
This is the same basic format as correlation maps such as MARSCOR3 produces,
except that multiple images are involved (thus the need for the index file,
in IDX).